Antibody Database Missing

[Ant-DA]

Hello to everyone,

I would like to use Rosetta to model an antibody, knowing heavy and light chains fasta sequences. However, downloading both the source code and the Ubuntu binaries, I cannot find the antibody database. I also checked in the database repository on GitHub. Does anyone know how to solve this? Thank you in advance

[jadolfbr]

Can you post your command? Have you compiled Rosetta or ran the binaries? Is it complaining about a database issue?

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On Fri, Jan 24, 2025 at 7:26 PM Ant-DA ***@***.***> wrote: Reopened #310 <#310>. — Reply to this email directly, view it on GitHub <#310>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZDHRGSI3RUPE3I4MIAJWT2MLK2TAVCNFSM6AAAAABV2XR6X6VHI2DSMVQWIX3LMV45UABFIRUXGY3VONZWS33OIV3GK3TUHI5E433UNFTGSY3BORUW63R3GE3TIMZZHE2A> . You are receiving this because you are subscribed to this thread.Message ID: <RosettaCommons/rosetta/repo-discussions/310/discussion_event/1743994@ github.com>

[Ant-DA]

I am working on PyRosetta through Colab. These are my commands:

database = ".../main/database"
import pyrosetta
pyrosetta.init(extra_options=f"-database {database}")
from pyrosetta import pose_from_sequence

heavy_chain = "QVQLVQSGAEVKK..."
light_chain = "DVVMTQSPLSLPVTPGEP..."

heavy_chain_pose = pose_from_sequence(heavy_chain, "antibody")
light_chain_pose = pose_from_sequence(light_chain, "antibody")

I get the following error: "Unable to open file: .../main/database/chemical/residue_type_sets/antibody/residue_types.txt"

I cannot file this file into the database (I also double checked on github). I downloaded both the source code and ubuntu binaries.

Thank you for your help!

[jadolfbr]

Remove the ‘antibody’ string from pose_from_sequence. Once you have that though, not sure what modeling you will be doing with that pose - are you following a tutorial? Are you trying to use RosettaAntibody to model (I’m not 100% sure the full protocol is in PyRosetta, but I’ll check)

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-Jared

On Sun, Jan 26, 2025 at 6:14 AM Ant-DA ***@***.***> wrote: I am working on PyRosetta through Colab. These are my commands: database = ".../main/database" import pyrosetta pyrosetta.init(extra_options=f"-database {database}") from pyrosetta import pose_from_sequence heavy_chain = "QVQLVQSGAEVKK..." light_chain = "DVVMTQSPLSLPVTPGEP..." heavy_chain_pose = pose_from_sequence(heavy_chain, "antibody") light_chain_pose = pose_from_sequence(light_chain, "antibody") I get the following error: "Unable to open file: .../main/database/chemical/residue_type_sets/antibody/residue_types.txt" I cannot file this file into the database (I also double checked on github). I downloaded both the source code and ubuntu binaries. Thank you for your help! — Reply to this email directly, view it on GitHub <#310 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZDHRAX3Z6QNIP4LDPCXUD2MS7QBAVCNFSM6AAAAABV2XR6X6VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTCOJVG42DONQ> . You are receiving this because you commented.Message ID: ***@***.***>

[Ant-DA]

My objective is to model an antibody knowing the FASTA sequences of the heavy and light chains. Then, I woul like to model the docking between the antibody and the ligand. Could you suggest me any tutorial about this? This is my first time approaching to the "antibody" world and I would like to discover more about it. Thank you for your time, I really appreciate your help.

[jadolfbr]

Honestly, at this point, just use AntibodyBuilder2 that is part of the ImmuneBuilder suite. It’s fast, accurate, and free.

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-Jared

On Sun, Jan 26, 2025 at 5:43 PM Ant-DA ***@***.***> wrote: My objective is to model an antibody knowing the FASTA sequences of the heavy and light chains. Then, I woul like to model the docking between the antibody and the ligand. Could you suggest me any tutorial about this? This is my first time approaching to the "antibody" world and I would like to discover more about it. Thank you for your time, I really appreciate your help. — Reply to this email directly, view it on GitHub <#310 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZDHRBW67KQJQPTTJYZW7L2MVQJ7AVCNFSM6AAAAABV2XR6X6VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTCOJWGI3DQOA> . You are receiving this because you commented.Message ID: ***@***.***>